1. Lack of configurability. And here I do not mean lack of eyecandy galore; I mean you cannot do simple things like changing the font size - not without installing hundreds of MB of additional packages, running dodgy third-party utilities, or mucking around in dconf-editor. That's not simple, it is the precise antithesis of simplicity - it makes life hard for end users, particularly end users who cannot use the default interface settings for whatever reason. And that is really hypocritical for "Linux for human beings."

2. Clickiness. I'm not particularly enamored with Gnome 3, but launching stuff in it is fast; the launcher displays all your applications in a giant alphabetical list, and you can narrow them down by category with buttons on the side. It actually works fairly well... Whereas in Unity, the developers were in a hurry to remove the distinction between local applications and ones in the repository, for gods only know what reason. Which means you have to click-click-click through lots of buttons to get a full list of installed applications. That is bad. Users should never, ever get "lost" in the desktop with no idea where something is. All installed applications should be immediately obvious, and available applications that are not installed should be clearly designated as such, to avoid confusion and clutter. This is not stodgy interface conservatism, this is common sense.

There are other problems, of course, but I don't think any are as severe as those.